Very, very carefully.
We can't just toss context to the wind with this. Games has historically been heavily skewed towards the empowerment fantasy, and though games don't cause violence, viewing Columbine's shooting through the lens of an empowerment fantasy can VERY easily amount to something horribly insensitive. That's not political correctness in the negative sense that term is usually used, its an acknowledgement that in context, this would be an INCREDIBLY difficult undertaking. You would need to make a game that engages the player in a different way, or in a way that subverts traditional the traditional aesthetics. Your probably looking at a horror game, a subversive action game along the lines of Spec Ops, or an abstract, "Art game". And you will probably have to look at an aspect of the shooting, not the shooting as a whole.
I can see a short, survival horror game where you play as a potential victim. Old school, powerless, Amnesia style horror. But I think it would feel sort of empty without a deeper point to make, and without a deeper point to make, the specter of a power fantasy may rear its ugly head and ruin what the game might say. So I see it as a series of, "Puzzles", where you take on the role of various students and teachers at the school, but in addition to solving a challenge, you have to figure out what your goal can be. One, "Level" may involve escaping, while in another, avoiding death may be impossible. In another, perhaps you chose between surviving or saving someone else, and saving someone unlocks that persons level, which again, could end in inevitable death. There would be an amount of randomness, so you never know if there was a possibility to do something better, and ultimately, it will always be a tragedy. All consequences would be qualitative, so there is no points or tallys, just a series of events which the players themselves make a judgement on. It may make the game more frusterating, but the mechanics would support the concept of hope even in the face of hopelessness. Even if you are doomed, you still have to try, because it is worth trying, and both the tragedy of facing those choices and the perseverance to try to overcome that tragedy. Also, it would need to be permadeath with no saving, and the game would have to be rather short to compensate for the frustration. That would communicate the loss of control that victims would experience to the audience
A game from the shooters perspective is EXTREMELY dicey. It's very hard not to glamorize. Adding a layer of fantasy, then ripping away the fantasy and leaving the player profoundly uncomfortable (The Spec Ops route) could work, but it would take brass balls to stand behind your work and explain why what you are doing is subversive, and not praise. And you would have to go all in to make the player feel uncomfortable. Frankly, you could finish the game, and the game could come across as a glorification of violence, and the exact opposite of what you wanted. I gotta say that anyone who tried this is braver then I am.
Another option, and I'm even more fuzzy on how to do THIS, would be to glamorize the shooting, but make clear that the glamour is seen from the perspective of the media portrayal. One way I imagine this is to make the game in 2 distinct visual and play styles. In one, everything is done like an action movie, but from the bad guys perspective. Mow down people throwing objects at you 90's arcade shooter style, get a high score and the like, basically the most sickening portrayal of the shooting as a power fantasy you can imagine. The other if just people slowly leaving the room that you can shoot at whim, washed out colors, no music, tinny sound, horrible crying and screaming and no challenge whatsoever. Only have the glorified action sequence when you can see a news camera from out of a window. At the end, make a badass-looking scene where the shooter puts the gun to his head, and just before he pulls the trigger, go back to the realistic, depressing style, a brief moment of shock as the trigger is pulled, and show just a dead body and a fade to black.
Id try to come up with ideas for a more abstract, art game way to represent the shooting but honestly, I was saving that for exploring the shooters actual motivations, but...this exercise was way to depressing, and doing that would be the most depressing of all.